The initial search was TBlastN [ 16] at JGI (http://genome.jgi-psf.org/pages/blast.jsf?db=Emihu1) with the following parameters changed: Target database: Emiliania huxleyi v1 scaffolds (unmasked), 'Filter low complexity regions' off, and 'Perform gapped alignment' on.
Sequences of primers for all other loci were designed using Primer3 [ 63] with the following parameters changed from default: Primer size = 20,22,27 (minimum, optimal, maximum); Primer Tm = 62°C, 65°C, 68°C (minimum, optimal, maximum); Max Tm difference = 2.5°C; CG clamp = 1.
The following parameters were changed and compared with two reference sessions: feed force, working direction, vibration level, balance and the use of an additional handle.
For tRNAscan-SE, the following parameters were changed: organism = "Nematode Mito", origin = yes, ace = yes; fops = yes, breakdown = yes, gcode ="Invertebrate Mito", covescore = 0.1, euparams = relaxed.
The following parameters were changed from default settings: -fastMap, -minIdentity = 99, -maxIntron = 5, and -minScore = 30 (87% of the CENH3 reads and 82% of the control reads could be aligned with the much more stringent setting -minScore = 300).
In order to check the robustness, following parameters were deliberately changed at three different concentration levels (300, 500 and 800 ng of each standard), scanning wavelength (λmax ± 2nm), mobile phase volume (15 ± 2 mL), and time variation (30 minutes) before chromatographic process, were studied and effects on the results were examined.
In order to check the robustness, following parameters were intentionally changed within the range of ± 5% at three different concentration levels (300, 500 and 700 ng); mobile phase composition, time from spotting to chromatography, time from chromatography to scanning and chamber saturation time and using different type of TLC plates.
In order to check the robustness, following parameters were deliberately changed within the range of ± 5% at three different concentration levels (200, 400 and 800 ng); amount of mobile phase, mobile phase composition, time from spotting to chromatography, time from chromatography to scanning and chamber saturation time.
Secondary outcomes of this study will be (change in) the following parameters between baseline (T0) and follow-up (T1, T2), comparing the NC-group with the UC-group: If chemotherapy is continued after three cycles of CAPOX −B) or four cycles of FOLFOX −B), change in skeletal muscle area at L3 will also be determined using CT-scans after six cycles of CAPOX −B) or eight cycles of FOLFOX −B).
Based on the discussions in the previous subsection, we change the following parameters related to the fragments.
